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formatting_help
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This manuscript is a template (aka "rootstock") for [Manubot](https://manubot.org/ "Manubot"), a tool for writing scholarly manuscripts.
Use this template as a starting point for your manuscript.
The rest of this document is a full list of formatting elements/features supported by Manubot.
Compare the input (`.md` files in the `/content` directory) to the output you see below.
## Basic formatting
**Bold** __text__
[Semi-bold text]{.semibold}
[Centered text]{.center}
[Right-aligned text]{.right}
*Italic* _text_
Combined *italics and __bold__*
~~Strikethrough~~
1. Ordered list item
2. Ordered list item
a. Sub-item
b. Sub-item
i. Sub-sub-item
3. Ordered list item
a. Sub-item
- List item
- List item
- List item
subscript: H~2~O is a liquid
superscript: 2^10^ is 1024.
[unicode superscripts](https://www.google.com/search?q=superscript+generator)⁰¹²³⁴⁵⁶⁷⁸⁹
[unicode subscripts](https://www.google.com/search?q=superscript+generator)₀₁₂₃₄₅₆₇₈₉
A long paragraph of text.
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.
Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
Putting each sentence on its own line has numerous benefits with regard to [editing](https://asciidoctor.org/docs/asciidoc-recommended-practices/#one-sentence-per-line) and [version control](https://rhodesmill.org/brandon/2012/one-sentence-per-line/).
Line break without starting a new paragraph by putting
two spaces at end of line.
## Document organization
Document section headings:
# Heading 1
## Heading 2
### Heading 3
#### Heading 4
##### Heading 5
###### Heading 6
### A heading centered on its own printed page{.center .page_center}
<!-- an arbitrary comment. visible in input, but not visible in output. -->
Horizontal rule:
---
`Heading 1`'s are recommended to be reserved for the title of the manuscript.
`Heading 2`'s are recommended for broad sections such as *Abstract*, *Methods*, *Conclusion*, etc.
`Heading 3`'s and `Heading 4`'s are recommended for sub-sections.
## Links
Bare URL link: <https://manubot.org>
[Long link with lots of words and stuff and junk and bleep and blah and stuff and other stuff and more stuff yeah](https://manubot.org)
[Link with text](https://manubot.org)
[Link with hover text](https://manubot.org "Manubot Homepage")
[Link by reference][manubot homepage]
[Manubot Homepage]: https://manubot.org
## Citations
Citation by DOI [@doi:10.7554/eLife.32822].
Citation by PubMed Central ID [@pmc:PMC6103790].
Citation by PubMed ID [@pubmed:30718888].
Citation by Wikidata ID [@wikidata:Q56458321].
Citation by ISBN [@isbn:9780262517638].
Citation by URL [@{https://greenelab.github.io/meta-review/}].
Citation by alias [@deep-review].
Multiple citations can be put inside the same set of brackets [@doi:10.7554/eLife.32822; @deep-review; @isbn:9780262517638].
Manubot plugins provide easier, more convenient visualization of and navigation between citations [@doi:10.1371/journal.pcbi.1007128; @pubmed:30718888; @pmc:PMC6103790; @deep-review].
Citation tags (i.e. aliases) can be defined in their own paragraphs using Markdown's reference link syntax:
[@deep-review]: doi:10.1098/rsif.2017.0387
## Referencing figures, tables, equations
Figure @fig:square-image
Figure @fig:wide-image
Figure @fig:tall-image
Figure @fig:vector-image
Table @tbl:bowling-scores
Equation @eq:regular-equation
Equation @eq:long-equation
## Quotes and code
> Quoted text
> Quoted block of text
>
> Two roads diverged in a wood, and I—
> I took the one less traveled by,
> And that has made all the difference.
Code `in the middle` of normal text, aka `inline code`.
Code block with Python syntax highlighting:
```python
from manubot.cite.doi import expand_short_doi
def test_expand_short_doi():
doi = expand_short_doi("10/c3bp")
# a string too long to fit within page:
assert doi == "10.25313/2524-2695-2018-3-vliyanie-enhansera-copia-i-insulyatora-gypsy-na-sintez-ernk-modifikatsii-hromatina-i-svyazyvanie-insulyatornyh-belkov-vtransfetsirovannyh-geneticheskih-konstruktsiyah"
```
Code block with no syntax highlighting:
```
Exporting HTML manuscript
Exporting DOCX manuscript
Exporting PDF manuscript
```
## Figures
{#fig:square-image}
{#fig:wide-image}
{#fig:tall-image height=3in}
{#fig:vector-image height=2.5in .white}
## Tables
| *Bowling Scores* | Jane | John | Alice | Bob |
|:-----------------|:-------------:|:-------------:|:-------------:|:-------------:|
| Game 1 | 150 | 187 | 210 | 105 |
| Game 2 | 98 | 202 | 197 | 102 |
| Game 3 | 123 | 180 | 238 | 134 |
Table: A table with a top caption and specified relative column widths.
{#tbl:bowling-scores}
| | Digits 1-33 | Digits 34-66 | Digits 67-99 | Ref. |
|:--------|:-----------------------------------|:----------------------------------|:----------------------------------|:------------------------------------------------------------|
| pi | 3.14159265358979323846264338327950 | 288419716939937510582097494459230 | 781640628620899862803482534211706 | [`piday.org`](https://www.piday.org/million/) |
| e | 2.71828182845904523536028747135266 | 249775724709369995957496696762772 | 407663035354759457138217852516642 | [`nasa.gov`](https://apod.nasa.gov/htmltest/gifcity/e.2mil) |
Table: A table too wide to fit within page.
{#tbl:constant-digits}
| | **Colors** <!-- $colspan="2" --> | |
|:--------:|:--------------------------------:|:--------------------:|
| **Size** | **Text Color** | **Background Color** |
| big | blue | orange |
| small | black | white |
Table: A table with merged cells using the `attributes` plugin.
{#tbl: merged-cells}
## Equations
A LaTeX equation:
$$\int_0^\infty e^{-x^2} dx=\frac{\sqrt{\pi}}{2}$$ {#eq:regular-equation}
An equation too long to fit within page:
$$x = a + b + c + d + e + f + g + h + i + j + k + l + m + n + o + p + q + r + s + t + u + v + w + x + y + z + 1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9$$ {#eq:long-equation}
## Special
<i class="fas fa-exclamation-triangle"></i> [WARNING]{.semibold} _The following features are only supported and intended for `.html` and `.pdf` exports._
_Journals are not likely to support them, and they may not display correctly when converted to other formats such as `.docx`._
[Link styled as a button](https://manubot.org "Manubot Homepage"){.button}
Adding arbitrary HTML attributes to an element using Pandoc's attribute syntax:
::: {#some_id_1 .some_class style="background: #ad1457; color: white; margin-left: 40px;" title="a paragraph of text" data-color="white" disabled="true"}
Manubot Manubot Manubot Manubot Manubot.
Manubot Manubot Manubot Manubot.
Manubot Manubot Manubot.
Manubot Manubot.
Manubot.
:::
Adding arbitrary HTML attributes to an element with the Manubot `attributes` plugin (more flexible than Pandoc's method in terms of which elements you can add attributes to):
Manubot Manubot Manubot Manubot Manubot.
Manubot Manubot Manubot Manubot.
Manubot Manubot Manubot.
Manubot Manubot.
Manubot.
<!-- $id="element_id" class="some_class" $style="color: #ad1457; margin-left: 40px;" $disabled="true" $title="a paragraph of text" $data-color="red" -->
Available background colors for text, images, code, banners, etc:
`white`{.white}
`lightgrey`{.lightgrey}
`grey`{.grey}
`darkgrey`{.darkgrey}
`black`{.black}
`lightred`{.lightred}
`lightyellow`{.lightyellow}
`lightgreen`{.lightgreen}
`lightblue`{.lightblue}
`lightpurple`{.lightpurple}
`red`{.red}
`orange`{.orange}
`yellow`{.yellow}
`green`{.green}
`blue`{.blue}
`purple`{.purple}
Using the [Font Awesome](https://fontawesome.com/) icon set:
<!-- include the Font Awesome library, per: https://fontawesome.com/start -->
<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.7.2/css/all.css">
<i class="fas fa-check"></i> <i class="fas fa-question"></i> <i class="fas fa-star"></i> <i class="fas fa-bell"></i> <i class="fas fa-times-circle"></i> <i class="fas fa-ellipsis-h"></i>
[
<i class="fas fa-scroll fa-lg"></i> **Light Grey Banner**<br>
useful for *general information* - [manubot.org](https://manubot.org/)
]{.banner .lightgrey}
[
<i class="fas fa-info-circle fa-lg"></i> **Blue Banner**<br>
useful for *important information* - [manubot.org](https://manubot.org/)
]{.banner .lightblue}
[
<i class="fas fa-ban fa-lg"></i> **Light Red Banner**<br>
useful for *warnings* - [manubot.org](https://manubot.org/)
]{.banner .lightred}